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Normalised coverage

Merged Normalised coverage
normalised_coverage into master
1 unresolved thread
Merged Dominik Burri requested to merge normalised_coverage into master
1 unresolved thread

Added snakemake rules to create normalised coverage. Addresses #45 (closed).

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Pipeline passed for 5f857a82 on normalised_coverage

Merged by BIOPZ-Gypas FoivosBIOPZ-Gypas Foivos 5 years ago (Mar 6, 2020 2:58pm UTC)

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Pipeline #10397 passed

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Pipeline passed for 2dfb1c2c on master

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workflow/rules/paired_end.snakefile.smk
453 453 {params.directionality} \
454 454 {input.reads1} {input.reads2} > {output.pseudoalignment}) \
455 455 2> {log.stderr}"
456
  • Alex Kanitz
    Alex Kanitz @kanitz ·
    Owner

    @gypas @burri0000 The rules for paired and single end libraries are exactly the same I think, except for the strings/names "single" and "paired" and some random whitespace at line ends. Couldn't we just put this rule in the common Snakefile in such cases?

  • Dominik Burri
    Dominik Burri @burri0000 ·
    Author Maintainer

    Yes, but then I would also put ALFA in the main Snakefile, because it does not depend on single or paired end, only on the directionality.

    We decided then to have them separate still.

  • BIOPZ-Gypas Foivos
    BIOPZ-Gypas Foivos @gypas ·
    Maintainer

    Yes you can also put that in the main Snakefile. The reason we put some rules separate is the inputs are different. If the input is the same for single and paired end reads, we can put one rule instead of two.

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  • BIOPZ-Gypas Foivos
    BIOPZ-Gypas Foivos @gypas ·
    Maintainer

    @kanitz Yes this is true for some other rules as well. e.g. index_genomic_alignment_samtools

    I might make some changes in another branch

  • Alex Kanitz
    Alex Kanitz @kanitz ·
    Owner

    @gypas Yeah, good idea. Let's try to avoid unnecessary code duplication. Hard to maintain and a big source of errors.

  • BIOPZ-Gypas Foivos
    BIOPZ-Gypas Foivos @gypas ·
    Maintainer

    @kanitz @burri0000 Here is the merge request about this: https://git.scicore.unibas.ch/zavolan_group/pipelines/rnaseqpipeline/-/merge_requests/38

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